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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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) 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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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) 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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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) 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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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) 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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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) 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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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) 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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ), 'gf_id' => 'HOM05D001133', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001133' ), 'data_identifier' => 'HOM05D001133', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001133', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '544', 'num_species' => '79' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31sc227G10' => 'aar', 'Actinidia34904' => 'ach', 'Ah.03g144250' => 'amhyb', 'Ah.10g027520' => 'amhyb', 'Ah.10g027850' => 'amhyb', 'Ah.10g028330' => 'amhyb', 'AL2G20669' => 'aly', 'AL2G21070' => 'aly', 'AL2G21520' => 'aly', 'Aqoxy4G01524' => 'aox', 'Aqoxy6G02208' => 'aox', 'Aqoxy7G01722' => 'aox', 'arahy.Tifrunner.gnm1.ann1.52FDNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.99IIFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EU0XZY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F1ZVR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IS7HAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4P4RT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH74DG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VD5UEC' => 'arhy', 'AT2G07732' => 'ath', 'ATCG00490' => 'ath', 'ATMG00280' => 'ath', 'ATR0303G005' => 'atr', 'ATR0443G001' => 'atr', 'ATR0559G032' => 'atr', 'ATR0626G377' => 'atr', 'ATR0661G257' => 'atr', 'ATR1156G051' => 'atr', 'Atru.chr7.148' => 'acertr', 'AUR62006113' => 'cqu', 'AUR62032525' => 'cqu', 'AUR62044378' => 'cqu', 'BcaC03g15275' => 'bca', 'BcaC03g16537' => 'bca', 'BcaC03g16539' => 'bca', 'BcaC03g16542' => 'bca', 'BcaC04g20702' => 'bca', 'BcaC04g21283' => 'bca', 'BcaC05g26869' => 'bca', 'BcaC05g26895' => 'bca', 'BcaC08g43701' => 'bca', 'BcaC08g43706' => 'bca', 'BcaNung04771' => 'bca', 'BNapus_Darmor_BZH_scaffold_234p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_253p00200' => 'bna', 'BNapus_Darmor_BZH_scaffold_287p00120' => 'bna', 'BolC6t36209H' => 'bol', 'BolC6t36212H' => 'bol', 'BolC7t41720H' => 'bol', 'BolSC28t60339H' => 'bol', 'BolSC28t60394H' => 'bol', 'BolSC28t60395H' => 'bol', 'BolSC29t60464H' => 'bol', 'BolSC29t60586H' => 'bol', 'BolSC35t60643H' => 'bol', 'BolSC35t60753H' => 'bol', 'BolSC45t60861H' => 'bol', 'BolSC45t60950H' => 'bol', 'BolSC46t60997H' => 'bol', 'BolSC46t61038H' => 'bol', 'BolSC47t61100H' => 'bol', 'BolSC47t61124H' => 'bol', 'BolSC49t61186H' => 'bol', 'BraA06t25424Z' => 'bra', 'BraSC140t45576Z' => 'bra', 'BraSC25t45845Z' => 'bra', 'BraSC25t45869Z' => 'bra', 'BraSC48t46263Z' => 'bra', 'BraSC48t46264Z' => 'bra', 'BraSC58t46418Z' => 'bra', 'BraSC58t46419Z' => 'bra', 'BraSC59t46594Z' => 'bra', 'BraSC77t46644Z' => 'bra', 'BraSC77t46645Z' => 'bra', 'BraSC77t46646Z' => 'bra', 'C02p43510' => 'bna', 'C03p92150' => 'bna', 'C09p40210' => 'bna', 'CAN.G1012.5' => 'can', 'CAN.G1183.4' => 'can', 'CAN.G1185.8' => 'can', 'CAN.G121.11' => 'can', 'CAN.G129.9' => 'can', 'CAN.G1478.1' => 'can', 'CAN.G1478.10' => 'can', 'CAN.G16.8' => 'can', 'CAN.G1634.3' => 'can', 'CAN.G1693.5' => 'can', 'CAN.G1859.1' => 'can', 'CAN.G1897.1' => 'can', 'CAN.G19.10' => 'can', 'CAN.G195.39' => 'can', 'CAN.G219.28' => 'can', 'CAN.G232.7' => 'can', 'CAN.G3.26' => 'can', 'CAN.G3.35' => 'can', 'CAN.G305.36' => 'can', 'CAN.G34.5' => 'can', 'CAN.G386.14' => 'can', 'CAN.G398.12' => 'can', 'CAN.G63.16' => 'can', 'CAN.G648.7' => 'can', 'CAN.G678.4' => 'can', 'CAN.G712.3' => 'can', 'CAN.G8.19' => 'can', 'CAN.G852.9' => 'can', 'CAN.G88.1' => 'can', 'CARHR282080' => 'chi', 'CARHR293420' => 'chi', 'CDE02G1327' => 'cde', 'CDE05G3428' => 'cde', 'Cfa021576' => 'cfa', 'ClCG03G001060' => 'cla', 'ClCG03G010150' => 'cla', 'ClCG04G000270' => 'cla', 'ClCG07G007510' => 'cla', 'ClCG11G009610' => 'cla', 'COL.COLO4_00354' => 'col', 'COL.COLO4_00506' => 'col', 'COL.COLO4_00933' => 'col', 'COL.COLO4_01314' => 'col', 'COL.COLO4_01577' => 'col', 'COL.COLO4_02298' => 'col', 'COL.COLO4_02308' => 'col', 'COL.COLO4_02576' => 'col', 'COL.COLO4_02584' => 'col', 'COL.COLO4_12471' => 'col', 'Cpa.g.sc11.171' => 'cpa', 'Cpa.g.sc11.172' => 'cpa', 'Cpa.g.sc63.21' => 'cpa', 'CsaV3_UNG203690' => 'csa', 'CsaV3_UNG209280' => 'csa', 'CSS0020155' => 'camsi', 'DCAR_022729' => 'dca', 'DCAR_023689' => 'dca', 'DCAR_029698' => 'dca', 'DCAR_032492' => 'dca', 'Dinv26731' => 'din', 'Dinv29307' => 'din', 'Duzib150G0123' => 'dzi', 'ECA054G0004' => 'eca', 'ECA074G0012' => 'eca', 'ECA077G0002' => 'eca', 'ECA232G3391' => 'eca', 'ECA236G4871' => 'eca', 'EL10Ac2g03510' => 'bvu', 'EL10Ac3g06000' => 'bvu', 'EL10Ac4g08027' => 'bvu', 'EL10Ac4g08323' => 'bvu', 'EL10Ac4g08324' => 'bvu', 'EL10Ac4g08325' => 'bvu', 'EL10Ac5g11253' => 'bvu', 'EL10Ac5g11663' => 'bvu', 'EL10Ac5g12382' => 'bvu', 'EL10Ac6g13459' => 'bvu', 'EL10Ac6g15082' => 'bvu', 'EL10Ac6g15083' => 'bvu', 'EL10Ac8g20234' => 'bvu', 'EL10As12g24025' => 'bvu', 'EL10As15g24118' => 'bvu', 'EL10As15g24120' => 'bvu', 'EL10As1g23052' => 'bvu', 'Eucgr.C03525' => 'egr', 'FAN02G1714' => 'fan', 'Gohir.1Z049899' => 'ghi', 'Gohir.A04G065755' => 'ghi', 'Gohir.A07G163645' => 'ghi', 'Gohir.A07G163681' => 'ghi', 'Gohir.A09G101500' => 'ghi', 'Gohir.A13G102850' => 'ghi', 'Gohir.D01G102320' => 'ghi', 'Gohir.D06G097150' => 'ghi', 'Gohir.D07G185900' => 'ghi', 'Gohir.D11G261000' => 'ghi', 'Gohir.D13G043750' => 'ghi', 'Gorai.001G206400' => 'gra', 'Gorai.006G014400' => 'gra', 'Gorai.007G279500' => 'gra', 'Gorai.010G112100' => 'gra', 'Gorai.012G005100' => 'gra', 'Gorai.013G048600' => 'gra', 'Gorai.013G111200' => 'gra', 'GSVIVG01013856001' => 'vvi', 'GSVIVG01022403001' => 'vvi', 'HanXRQChr00c0339g0573801' => 'han', 'HanXRQChr00c0702g0576841' => 'han', 'HanXRQChr00c0759g0577201' => 'han', 'HanXRQChr01g0009271' => 'han', 'HanXRQChr01g0020381' => 'han', 'HanXRQChr02g0041551' => 'han', 'HanXRQChr02g0044921' => 'han', 'HanXRQChr04g0111811' => 'han', 'HanXRQChr05g0144451' => 'han', 'HanXRQChr05g0144461' => 'han', 'HanXRQChr07g0200981' => 'han', 'HanXRQChr08g0210331' => 'han', 'HanXRQChr09g0276281' => 'han', 'HanXRQChr10g0283521' => 'han', 'HanXRQChr10g0283531' => 'han', 'HanXRQChr10g0284221' => 'han', 'HanXRQChr10g0289241' => 'han', 'HanXRQChr11g0326801' => 'han', 'HanXRQChr13g0413601' => 'han', 'HanXRQChr14g0435091' => 'han', 'HanXRQCPg0580011' => 'han', 'Hma1.2p1_0275F.1_g110896' => 'hma', 'Hma1.2p1_0275F.1_g110910' => 'hma', 'Hma1.2p1_0333F.1_g128105' => 'hma', 'Hma1.2p1_0815F.1_g222885' => 'hma', 'Hma1.2p1_1340F.1_g276670' => 'hma', 'HPP92_007193' => 'vpl', 'HPP92_011400' => 'vpl', 'HPP92_016587' => 'vpl', 'HPP92_019481' => 'vpl', 'HPP92_028398' => 'vpl', 'HPP92_028408' => 'vpl', 'Hund00265' => 'sun', 'Hund04032' => 'sun', 'Hund07991' => 'sun', 'Hund12657' => 'sun', 'Hund12954' => 'sun', 'Hund12955' => 'sun', 'Hund15469' => 'sun', 'Hund17419' => 'sun', 'Hund19841' => 'sun', 'Hund24028' => 'sun', 'Hund25914' => 'sun', 'Hund26969' => 'sun', 'Hund27445' => 'sun', 'Hund27487' => 'sun', 'Hund27569' => 'sun', 'Hund27601' => 'sun', 'Hund27663' => 'sun', 'Hund27706' => 'sun', 'Hund27872' => 'sun', 'Hund27909' => 'sun', 'Hund28033' => 'sun', 'Hund28092' => 'sun', 'Hund28099' => 'sun', 'Hund28116' => 'sun', 'Hund28169' => 'sun', 'Hund28245' => 'sun', 'Hund28253' => 'sun', 'Hund28287' => 'sun', 'Hund28299' => 'sun', 'Hund28475' => 'sun', 'Hund28495' => 'sun', 'Hund28509' => 'sun', 'Hund28710' => 'sun', 'Hund28724' => 'sun', 'Hund28737' => 'sun', 'Hund28817' => 'sun', 'Hund28818' => 'sun', 'Hund29131' => 'sun', 'Hund29144' => 'sun', 'Hund29173' => 'sun', 'Hund29212' => 'sun', 'Hund29494' => 'sun', 'Hund29639' => 'sun', 'Hund30194' => 'sun', 'Hund30196' => 'sun', 'Hund30346' => 'sun', 'Hund30348' => 'sun', 'Hund30353' => 'sun', 'Hund30395' => 'sun', 'Hund30414' => 'sun', 'Hund30455' => 'sun', 'Hund30567' => 'sun', 'Hund30595' => 'sun', 'Hund30616' => 'sun', 'Hund31095' => 'sun', 'Hund31101' => 'sun', 'Hund31106' => 'sun', 'Hund31113' => 'sun', 'Hund31157' => 'sun', 'Hund31165' => 'sun', 'Hund31168' => 'sun', 'Hund31189' => 'sun', 'Hund31191' => 'sun', 'Hund31218' => 'sun', 'Hund31298' => 'sun', 'Hund31316' => 'sun', 'Hund31358' => 'sun', 'Hund31373' => 'sun', 'Lalb_Chr07g0191521' => 'lal', 'Lalb_Chr07g0191531' => 'lal', 'Lalb_Chr07g0192641' => 'lal', 'Lalb_Chr07g0192651' => 'lal', 'Lalb_Chr07g0192661' => 'lal', 'Lalb_Chr13g0292761' => 'lal', 'Lalb_Chr13g0292771' => 'lal', 'Lalb_Chr13g0292911' => 'lal', 'Lalb_Chr13g0292921' => 'lal', 'Lalb_Chr15g0076081' => 'lal', 'Lalb_Chr19g0136111' => 'lal', 'Lalb_Chr20g0116011' => 'lal', 'Lalb_Chr25g0281541' => 'lal', 'Lalb_Chr25g0282001' => 'lal', 'Lj2A1239T193' => 'lonja', 'Lj2P1237T52' => 'lonja', 'Lj2P1239T147' => 'lonja', 'Lj4g0006327' => 'lja', 'Lj5P142T11' => 'lonja', 'LjContig00315g0013056' => 'lja', 'LjContig00318g0011153' => 'lja', 'Lsat_1_v5_gn_1_128061' => 'lsa', 'Lsat_1_v5_gn_2_70541' => 'lsa', 'Lsat_1_v5_gn_2_89801' => 'lsa', 'Lsat_1_v5_gn_3_109140' => 'lsa', 'Lsat_1_v5_gn_3_110220' => 'lsa', 'Lsat_1_v5_gn_3_130301' => 'lsa', 'Lsat_1_v5_gn_3_85740' => 'lsa', 'Lsat_1_v5_gn_4_102701' => 'lsa', 'Lsat_1_v5_gn_4_147641' => 'lsa', 'Lsat_1_v5_gn_6_82400' => 'lsa', 'Lsat_1_v5_gn_7_14980' => 'lsa', 'Lsat_1_v5_gn_7_98341' => 'lsa', 'Lsat_1_v5_gn_7_98361' => 'lsa', 'Lsat_1_v5_gn_8_44620' => 'lsa', 'Lsat_1_v5_gn_8_44640' => 'lsa', 'Lsat_1_v5_gn_9_11781' => 'lsa', 'Lsat_1_v5_gn_9_11801' => 'lsa', 'Mapoly0007s0124' => 'mpo', 'MD02G1049600' => 'mdo', 'MD07G1039000' => 'mdo', 'MD07G1110300' => 'mdo', 'MD11G1294900' => 'mdo', 'MD11G1295000' => 'mdo', 'Medtr0002s0100' => 'mtr', 'Medtr0002s0660' => 'mtr', 'Medtr1g059860' => 'mtr', 'Medtr2176s0010' => 'mtr', 'Medtr3g035490' => 'mtr', 'Medtr3g035680' => 'mtr', 'Medtr4g051270' => 'mtr', 'Medtr5g075460' => 'mtr', 'Medtr6g055010' => 'mtr', 'Medtr7g021770' => 'mtr', 'Medtr7g033770' => 'mtr', 'Medtr7g084780' => 'mtr', 'Medtr7g117930' => 'mtr', 'MELO3C000130.2' => 'cme', 'MELO3C000483.2' => 'cme', 'MELO3C012384.2' => 'cme', 'MELO3C026353.2' => 'cme', 'MELO3C027613.2' => 'cme', 'MELO3C027735.2' => 'cme', 'Migut.D01358' => 'egut', 'Migut.D01359' => 'egut', 'Migut.F01575' => 'egut', 'Nitab4.5_0000007g0300' => 'nta', 'Nitab4.5_0000266g0030' => 'nta', 'Nitab4.5_0000563g0060' => 'nta', 'Nitab4.5_0000825g0040' => 'nta', 'Nitab4.5_0000841g0020' => 'nta', 'Nitab4.5_0002183g0050' => 'nta', 'Nitab4.5_0002197g0020' => 'nta', 'Nitab4.5_0002204g0090' => 'nta', 'Nitab4.5_0002553g0010' => 'nta', 'Nitab4.5_0002755g0110' => 'nta', 'Nitab4.5_0003415g0060' => 'nta', 'Nitab4.5_0003644g0100' => 'nta', 'Nitab4.5_0004172g0130' => 'nta', 'Nitab4.5_0006084g0010' => 'nta', 'Nitab4.5_0006311g0020' => 'nta', 'Nitab4.5_0007173g0020' => 'nta', 'Nitab4.5_0009390g0010' => 'nta', 'Nitab4.5_0009663g0010' => 'nta', 'Nitab4.5_0009663g0020' => 'nta', 'Nitab4.5_0011882g0010' => 'nta', 'Nitab4.5_0020415g0010' => 'nta', 'Nitab4.5_0022455g0010' => 'nta', 'Nn010s41430' => 'nnu', 'Nn010s41431' => 'nnu', 'Nn021s41540' => 'nnu', 'Nn263s45939' => 'nnu', 'Nn265s45951' => 'nnu', 'Nn2g12582' => 'nnu', 'Nn3g16982' => 'nnu', 'Oeu012840.1' => 'oeu', 'Oeu039072.1' => 'oeu', 'Oeu054723.1' => 'oeu', 'Oeu054727.1' => 'oeu', 'Oeu058367.1' => 'oeu', 'Oeu058368.1' => 'oeu', 'Oeu062835.1' => 'oeu', 'Oeu062841.8' => 'oeu', 'Oeu062854.1' => 'oeu', 'Oeu062862.1' => 'oeu', 'Os01g0791033' => 'osa', 'Os01g0899425' => 'osa', 'Os05g0427800' => 'osa', 'Os10g0356000' => 'osa', 'Os12g0207600' => 'osa', 'Peaxi162Scf00097g00133' => 'pax', 'Peaxi162Scf00100g00314' => 'pax', 'Peaxi162Scf00405g01311' => 'pax', 'Peaxi162Scf00870g00212' => 'pax', 'PGR081G0015' => 'pgr', 'PGR111G0068' => 'pgr', 'PGSC0003DMG400033037' => 'stu', 'Phvul.003G029300' => 'pvu', 'Phvul.004G121633' => 'pvu', 'Phvul.004G151000' => 'pvu', 'Phvul.009G144500' => 'pvu', 'Phvul.011G089000' => 'pvu', 'Phvul.011G145300' => 'pvu', 'Potri.012G062601' => 'ptr', 'Potri.013G162700' => 'ptr', 'Potri.T005800' => 'ptr', 'Potri.T124301' => 'ptr', 'Prupe.7G029600' => 'ppe', 'Psat0s1330g0280' => 'psa', 'Psat0s1661g0040' => 'psa', 'Psat0s411g0040' => 'psa', 'Psat0s5127g0120' => 'psa', 'Psat2g136760' => 'psa', 'Psat2g138800' => 'psa', 'Psat5g033320' => 'psa', 'Psat5g033360' => 'psa', 'Psat5g167920' => 'psa', 'Psat5g168040' => 'psa', 'Psat6g145640' => 'psa', 'Psat7g230840' => 'psa', 'PSO017G0180' => 'pso', 'PSO017G0772' => 'pso', 'PSO017G5135' => 'pso', 'PSO063G3916' => 'pso', 'PSO548G0049' => 'pso', 'QL07p017870' => 'qlo', 'QL93p0311_0021' => 'qlo', 'QL93p0403_0058' => 'qlo', 'RcHm_v2.0_Chr5g0043001' => 'rch', 'RcHm_v2.0_Chr5g0043011' => 'rch', 'RcHm_v2.0_CPg0502111' => 'rch', 'RhsimPtG0000800' => 'rsi', 'Sabra10G0056400' => 'sbr', 'SabraPtG0003300' => 'sbr', 'SalBow1G5051' => 'sbo', 'Sc03g0005190' => 'sci', 'Sc03g0005660' => 'sci', 'Sc05g0004580' => 'sci', 'Sc12g0007900' => 'sci', 'Sc16g0004770' => 'sci', 'Sc22g0003420' => 'sci', 'Sed0006458' => 'sed', 'Sed0013840' => 'sed', 'Sed0017424' => 'sed', 'Sed0019800' => 'sed', 'Sed0021071' => 'sed', 'SEGI_02135' => 'sgi', 'SEGI_02423' => 'sgi', 'SEGI_03157' => 'sgi', 'SEGI_03806' => 'sgi', 'SEGI_03887' => 'sgi', 'SEGI_18912' => 'sgi', 'SEGI_20703' => 'sgi', 'SEGI_22847' => 'sgi', 'SEGI_22883' => 'sgi', 'SEGI_27150' => 'sgi', 'SEGI_32167' => 'sgi', 'SEGI_32654' => 'sgi', 'SEGI_33906' => 'sgi', 'SEGI_40273' => 'sgi', 'SEGI_41278' => 'sgi', 'SGA_v2.0_scaffold194G40764' => 'sas', 'SGA_v2.0_scaffold43G16476' => 'sas', 'SGA_v2.0_scaffold477G52215' => 'sas', 'SHI10627' => 'shi', 'SHI14263' => 'shi', 'SHI14264' => 'shi', 'SHI14265' => 'shi', 'SHI23889' => 'shi', 'SHI35929' => 'shi', 'SHI35949' => 'shi', 'SHI36538' => 'shi', 'SHI37744' => 'shi', 'SHI39189' => 'shi', 'SHI41354' => 'shi', 'SHI49180' => 'shi', 'SHI50220' => 'shi', 'SHI50417' => 'shi', 'SHI50619' => 'shi', 'SHI51609' => 'shi', 'SHI52582' => 'shi', 'SHI52612' => 'shi', 'SHI52685' => 'shi', 'SHI53590' => 'shi', 'SHI53717' => 'shi', 'SHI53745' => 'shi', 'SHI53897' => 'shi', 'SHI53946' => 'shi', 'SMO086G0057' => 'smo', 'Solyc00g500063.1' => 'sly', 'Solyc02g077860.1' => 'sly', 'Solyc04g039840.1' => 'sly', 'Solyc04g039845.1' => 'sly', 'Solyc07g021200.1' => 'sly', 'Solyc12g062420.2' => 'sly', 'Solyc12g062540.3' => 'sly', 'Solyc12g062550.1' => 'sly', 'Solyc12g062560.1' => 'sly', 'Sopen03g013700' => 'spe', 'Sopen04g010010' => 'spe', 'Sopen06g016980' => 'spe', 'Sopen07g010180' => 'spe', 'Sopen10g008570' => 'spe', 'Sopen10g009160' => 'spe', 'Sopen12g025740' => 'spe', 'Sp3g25600' => 'spa', 'Sp5g20270' => 'spa', 'Thhalv10010325m.g' => 'esa', 'TPR.G12989' => 'tpr', 'TPR.G22131' => 'tpr', 'TWI09G0835' => 'twi', 'unitig_87.g27942' => 'ugi', 'unitig_91.g26507' => 'ugi', 'vmacro22413' => 'vma', 'VMungo0291G0001' => 'vmu', 'VMungo0446G0002' => 'vmu', 'VMungo1383G2115' => 'vmu', 'Zm00001eb027490' => 'zma', 'Zm00001eb039150' => 'zma', 'Zm00001eb105250' => 'zma', 'Zm00001eb105260' => 'zma', 'Zm00001eb187470' => 'zma', 'Zm00001eb282050' => 'zma', 'Zm00001eb380210' => 'zma', 'Zm00001eb434690' => 'zma', 'Zm00001eb434910' => 'zma', 'Zm00001eb435060' => 'zma', 'Zm00001eb435180' => 'zma', 'Zm00001eb435390' => 'zma', 'Zm00001eb435650' => 'zma', 'Zm00001eb436750' => 'zma', 'Zm00001eb437070' => 'zma', 'Zm00001eb437190' => 'zma', 'Zm00001eb437970' => 'zma', 'Zm00001eb438360' => 'zma', 'Zm00001eb439980' => 'zma', 'Zm00001eb440340' => 'zma', 'Zm00001eb440790' => 'zma', 'Zm00001eb440970' => 'zma' ) $gf_id = 'HOM05D001133' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001133' ) $data_identifier = 'HOM05D001133' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 11, 'bna' => (int) 6, 'bol' => (int) 17, 'bra' => (int) 12, 'can' => (int) 29, 'chi' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 1, 'cla' => (int) 5, 'col' => (int) 10, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 1, 'dca' => (int) 4, 'din' => (int) 2, 'dzi' => (int) 1, 'eca' => (int) 5, 'bvu' => (int) 17, 'egr' => (int) 1, 'fan' => (int) 1, 'ghi' => (int) 11, 'gra' => (int) 7, 'vvi' => (int) 2, 'han' => (int) 21, 'hma' => (int) 5, 'vpl' => (int) 6, 'sun' => (int) 68, 'lal' => (int) 14, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 17, 'mpo' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 6, 'egut' => (int) 3, 'nta' => (int) 22, 'nnu' => (int) 7, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 12, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 2, 'sbo' => (int) 1, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 15, 'sas' => (int) 3, 'shi' => (int) 24, 'smo' => (int) 1, 'sly' => (int) 9, 'spe' => (int) 7, 'spa' => (int) 2, 'esa' => (int) 1, 'tpr' => (int) 2, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 22 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb440970' $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